1. She can't convince Bob she didn't write the message: it's written right there on Bob's phone, and he'd remember if he'd tamper with it.
2. If Bob starts showing Alice's message around, she can't pretend he misremembered, as would be possible with an oral conversation. She'd have to flat out call him a liar.
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> using a system that is deliberately designed to allow you to say something then deny having said it might also cause extra suspicion.
Not if everyone used such a system. There's a difference between building & using your own obscure deniable chat application, and WhatsApp and Signal themselves enabling this.
> In practice [repudiability] has very little value. It is unlikely that the feature is worth the extra risk of the complexity it would take to implement it.
Deniable schemes are not more complex.
There's just one simple condition: use Diffie-Hellman key exchanges instead of signatures. The result will likely be simpler than a scheme that relies on signatures. I've implemented both key exchanges and signatures with elliptic curves (X25519 and Ed25519 specifically), and I'm telling you, key exchange is significantly simpler and harder to get wrong. (For the anecdote, I screwed-up once in my cryptographic work, and it was the signatures).
See https://noiseprotocol.org for fairly simple key exchange based protocols, with various properties one might care about (key compromise impersonation, resistance against replay-attacks, anonymity to third parties…).